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Sample GSM4605845

Query DataSets for GSM4605845

Status

Public on Dec 31, 2022

Title

OV_16_01D_45_Lu_OV

Sample type

SRA

Source name

lung

Organism

Rattus norvegicus

Characteristics

treatment chemical: oil vapor
dose (oil vapor): 300ppm;6hours/day;4days/week;16days of exposure
strain: Sprague-Dawley
time: 1 day post-exposure
tissue: lung

Treatment protocol

Exposures were performed in a whole-body inhalation chamber. The rats were exposed by inhalation to filtered air or oil vapor particles (300 ppm, 6 hours/day for 1 day or 300 ppm, 6 hours/day, 4 days/week for 4 weeks). At post exposure time intervals of 1 and 28 days, the air and oil vapor exposed rats were euthanized. n=6 for all groups.

Growth protocol

Male Sprague-Dawley rats (Hilltop Lab Animals, Scottdale, PA), weighing approximately 200-250 g were used in this study which was conducted in an Association for Assessment and Accreditation of Laboratory Animal Care International approved animal facility (NIOSH, Morgantown, WV) following a protocol approved by the Animal Care and Use Committee. The rats were housed in pairs and maintained on a 12-hour light-dark cycle in a temperature (68-72oF) and humidity (30-70%) controlled room with free access to filtered tap water and HaCXan Teklad Global 18% protein rodent diet (Harlan Teklad; Madison, WI).

Extracted molecule

total RNA

Extraction protocol

Total RNA was isolated from a piece of the lung tissue using the miRNeasy Mini Kit (Qiagen, Inc, Valencia, CA) following the procedure provided by the manufacturer.
One microgram total RNA/sample was used to create sequencing libraries using the Illumina TruSeq® Stranded Total RNA Library Prep (Illumina, Inc., San Diego, CA) following the manufacturer's protocol. Briefly, following depletion of ribosomal RNA (rRNA), the RNA samples were purified, fragmented (68°C for 5 minutes), and primed for cDNA synthesis. The denatured and cleaved RNA fragments were purified using a bead cleanup and reverse transcribed into first strand cDNA using reverse transcriptase and random primers. While synthesizing the double stranded cDNA, dUPT was incorporated in place of dTTP followed by the addition of a single ‘A’ nucleotide to the 3 prime ends to facilitate proper adapter ligation to each sample. Indexing adapters provided in the library preparation kit were ligated to the ends of the ds cDNA. After adapter ligation, the samples were PCR amplified (12 cycles) to enrich the DNA fragments containing the adapter molecules and to enhance the amount of DNA in the library using a Veriti™ 96 Well Thermal Cycler (Applied Biosystems; Foster City, CA).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

OV_highDose_rawCounts.csv

Data processing

Basecalls were performed using bcl2fastq/2.19.
Sequence reads were trimmed using Trimmomatic/0.35 with the following parameters ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:60
All sequences were aligned to the Rattus norvegicus Rnor 6.0 genome from NCBI downloaded July 31, 2015 using HiSat2/2.1.0.
Raw gene counts were assigned using Samtools/1.8, Python/2.7.3 and HTSeq/0.6.1.
Genome_build: Rnor6.0
Supplementary_files_format_and_content: 2 csv files including raw counts in a matrix; one file for high dose samples; one file for low dose samples

Submission date

Jun 10, 2020

Last update date

Dec 31, 2022

Contact name

Christina M Umbright

Organization name

DHHS/PHS/CDC/NIOSH

Department

HELD

Lab

L-4324